Background: Sierra Leone’s public health system struggles with its supply chain, which often leads to frequent stockouts, expiry, and pilferage of healthcare commodities. A well-coordinated supply chain system can minimize these challenges. Our current study explored the facilitators and barriers to pharmaceutical supply chain integration in Sierra Leone. Method: This qualitative study utilised the theory of saturation and a purposive sampling method to recruit 15 key informants from various districts in Sierra Leone. A semi-structured interview guide was used to conduct an in-depth interview using a recorder. The interview process was carried out at the various offices of readily available participants and online for out-of-reach participants who had a stable network. The recordings were transcribed verbatim, and themes and subthemes were identified from the transcripts. Result: The main factors facilitating the integration of the pharmaceutical supply chain included the availability of digital health tools, existing capacity-building initiatives, the presence of well-defined policies and Standard Operating Procedures, good working relationships with partners, and effective communication among stakeholders. Barriers such as poor financial allocation and reliance on external donors for support, Inadequate warehouse space, Fragmented procurement processes and logistical challenges, lack of adequate human resources, inconsistencies in policy implementation across regions, lack of timely information sharing and concerns over data security were the key barriers identified in our study. Conclusion: While there are facilitating factors which drive the supply chain integration process by reducing workload, streamlining data access, enhancing transparency, and fostering collaboration with partners; the existence of systemic barriers hinders the full realization of this process. Addressing these systemic barriers while leveraging the identified facilitators will be a crucial step towards building a functional and more resilient supply chain system with integrated functions to meet the country’s healthcare delivery goals.